HOw do i change to digest mode?

This is too much

Quoting Mark Jenkinson <[log in to unmask]>:

> Hi,
>
> We recommend you use flirt with the -applyxfm option to reapply a flirt
> matrix.  The conventions of the coordinates used by flirt are not entirely
> trivial, and they do depend a little on the nifti qform/sform information.
>
> If you are desperate to use your own matlab implementation then there
> is a thread on doing exactly this a little while ago (at least 4 months)
> in the FSL list.
>
> All the best,
> 	Mark
>
>
>
> On 6 May 2010, at 22:19, Dan Golding wrote:
>
>> Hi all,
>>
>> I need to reapply the affine transformation generated by flirt on  
>> different data (dti fibres). I think it should be quite straight  
>> forward. I have been trying to reapply the transformation myself to  
>> the t1 data that I used flirt on just to make certain I understand  
>> it properly and I can't seem to get the same output image.
>>
>> I think it has something to do with the fact that I completely  
>> ignore all the information in the nifti header. Is there anything  
>> in there that I have to consider before applying the affine  
>> transformation?
>>
>> Here is the matlab script I have been using - perhaps someone can  
>> see where I have gone wrong?
>>
>> -----------------------------------------------------------------------------------------------------------------------------------------------------------
>> %Load the affine transformation matirx from flirt
>> load e2fflirt -ASCII;
>> A = e2fflirt;
>>
>> %load the source image
>> source = load_nii('EF1T_t1.nii');
>>
>> %make an empty output image
>> output = source;
>> output.img = output.img*0;
>>
>> Io = output.img;
>> Is = source.img;
>>
>> %find the output image dimensions so we know how many voxels to  
>> iterate through
>> OutDim = size(output.img);
>>
>> %Iterate through each output voxel
>> for i = 1:OutDim(1)
>>   for j = 1:OutDim(2)
>>       for k = 1:OutDim(3)
>>
>>           %Perfom the affine transformation on voxel (i,j,k). Note that
>>           %half of the size of each dimension is subtracted, this is so
>>           %that the centre of rotation is in the centre of the image
>>           %rather than at voxel (0,0,0).
>>           Y = A*[i - OutDim(1)/2 + 1; j - OutDim(2)/2 + 1; k -  
>> OutDim(3)/2 + 1; 1];
>>
>>               %This is used for trilinear interpolation
>>               id = mod(Y(1),1);
>>               jd = mod(Y(2),1);
>>               kd = mod(Y(3),1);
>>
>>               %Add half the dimension back so voxel don't half -ve
>>               %coordinates.
>>               Y = floor(Y + [OutDim'./2;0]);
>>
>>           try
>>               %------------------------------------------------
>>               %Warping output locations to source
>>
>>               %Trilinear -- I've tested this, it definitely works
>>               C = Is(Y(1):Y(1)+1,Y(2):Y(2)+1,Y(3):Y(3)+1);
>>               Io(i,j,k) = (1-kd)*((1-jd)*((1-id)*C(1,1,1) +  
>> id*C(2,1,1)) + jd*((1-id)*C(1,2,1) + id*C(2,2,1))) +  
>> kd*((1-jd)*((1-id)*C(1,1,2) + id*C(2,1,2)) + jd*((1-id)*C(1,2,2) +  
>> id*C(2,2,2)));
>>
>>               %Nearest Neighbour
>>                %Io(i,j,k) = Is(Y(1), Y(2), Y(3));
>>
>>           catch ERR %in the cases where the vectors point off the  
>> image, i.e. I,J,K == 0 | 160(200) as the case may be
>>
>>               continue;
>>           end;
>>
>>       end;
>>   end;
>> end;
>>
>> %put the image back into a nifti structure. Note that the image is warped
>> %but the header remains the same as the source image!
>> output.img = Io;
>> -----------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>>
>> Any suggestions are welcome
>>
>> Kind Regards
>> Dan Golding
>>
>